Table Of ContentCompendium of Plant Genomes
Series Editor: Chittaranjan Kole
Suguru Tsuchimoto Editor
The Jatropha
Genome
Compendium of Plant Genomes
Series Editor
Chittaranjan Kole, Raja Ramanna Fellow, Department of Atomic Energy,
Government of India, Kalyani, India
Whole-genome sequencing is at the cutting edge of life sciences in the new
millennium.SincethefirstgenomesequencingofthemodelplantArabidopsis
thaliana in 2000, whole genomes of about 70 plant species have been
sequenced and genome sequences ofseveral other plants arein the pipeline.
Research publications onthesegenomeinitiatives arescattered ondedicated
web sites and in journals with all too brief descriptions. The individual
volumes elucidate the background history of the national and international
genome initiatives; public and private partners involved; strategies and
genomicresourcesandtoolsutilized;enumerationonthesequencesandtheir
assembly; repetitive sequences; gene annotation and genome duplication. In
addition,syntenywithothersequences,comparisonofgenefamiliesandmost
importantly potential of the genome sequence information for gene pool
characterization andgenetic improvementof cropplantsare described.
More information about this series at http://www.springer.com/series/11805
Suguru Tsuchimoto
Editor
The Jatropha Genome
123
Editor
SuguruTsuchimoto
Graduate Schoolof Engineering
Osaka University
Suita,Osaka
Japan
ISSN 2199-4781 ISSN 2199-479X (electronic)
Compendium of Plant Genomes
ISBN978-3-319-49651-1 ISBN978-3-319-49653-5 (eBook)
DOI 10.1007/978-3-319-49653-5
LibraryofCongressControlNumber:2017939319
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This book series is dedicated to
my wife Phullara, and our children Sourav,
and Devleena
Chittaranjan Kole
Preface to the Series
Genome sequencing has emerged as the leading discipline in the plant sci-
encescoincidingwiththestartofthenewcentury.Formuchofthetwentieth
century, plant geneticists were only successful in delineating putative chro-
mosomallocation,function,andchanges ingenes indirectlythroughtheuse
ofanumberof‘markers’physicallylinkedtothem.Theseincludedvisibleor
morphological,cytological,protein,andmolecularorDNAmarkers.Among
them,thefirstDNAmarker,theRFLPs,introducedarevolutionarychangein
plantgeneticsandbreedinginthemid-1980s,mainlybecauseoftheirinfinite
number and thus potential to cover maximum chromosomal regions, phe-
notypic neutrality, absence of epistasis, and codominant nature. An array of
other hybridization-based markers PCR-based markers, and markers based
on both facilitated construction of genetic linkage maps, mapping of genes
controlling simply inheritedtraits andevengeneclusters(QTLs) controlling
polygenic traits in a large number of model and crop plants. During this
periodanumberofnewmappingpopulationsbeyondF wereutilizedanda
2
number of computer programs were developed for map construction, map-
ping of genes, and for mapping of polygenic clusters or QTLs. Molecular
markerswerealsousedinstudiesofevolutionandphylogeneticrelationship,
genetic diversity, DNA-fingerprinting and map-based cloning. Markers
tightly linked to the genes were used in crop improvement employing the
so-called marker-assisted selection. These strategies of molecular genetic
mapping and molecular breeding made a spectacular impact during the last
one and a half decades of the twentieth century. But still they remained
‘indirect’ approaches for elucidation and utilization of plant genomes since
much of the chromosomes remained unknown and the complete chemical
depiction of them was yet to be unraveled.
Physical mapping of genomes was the obvious consequence that facili-
tated development of the ‘genomic resources’ including BAC and YAC
libraries to develop physical maps in some plant genomes. Subsequently,
integrated genetic-physical maps were also developed in many plants. This
led to the concept of structural genomics. Later on, emphasis was laid on
EST and transcriptome analysis to decipher the function of the active gene
sequences leading to another concept defined as functional genomics. The
advent of techniques of bacteriophage gene and DNA sequencing in the
1970s was extended to facilitate sequencing of these genomic resources in
the last decade of the twentieth century.
vii
viii PrefacetotheSeries
As expected, sequencing of chromosomal regions would have led to too
muchdatatostore,characterize,andutilizewiththe-thenavailablecomputer
softwarecouldhandle.Butdevelopmentofinformationtechnologymadethe
life of biologists easier by leading to a swift and sweet marriage of biology
and informatics and a new subject was born—bioinformatics.
Thus, evolution of the concepts, strategies and tools of sequencing and
bioinformaticsreinforcedthesubjectofgenomics—structuralandfunctional.
Today, genome sequencing has traveled much beyond biology and involves
biophysics, biochemistry and bioinformatics!
Thanks to the efforts of both public and private agencies, genome
sequencingstrategiesareevolving veryfast,leadingtocheaper, quickerand
automated techniquesright from clone-by-clone andwhole-genomeshotgun
approaches to a succession of second generation sequencing methods.
Development of software of different generations facilitated this genome
sequencing. At the same time, newer concepts and strategies were emerging
to handle sequencing of the complex genomes, particularly the polyploids.
Itbecamearealitytochemically—andsodirectly—defineplantgenomes,
popularly called whole-genome sequencing or simply genome sequencing.
The history of plant genome sequencing will always cite the sequencing
of the genome of the model plant Arabidopsis thaliana in 2000 that was
followedbysequencingthegenomeofthecropandmodelplantricein2002.
Since then, the number of sequenced genomes of higher plants has been
increasing exponentially, mainly due to the development of cheaper and
quicker genomic techniques and, most importantly, development of collab-
orative platforms such as national and international consortia involving
partners from public and/or private agencies.
AsIwritethisprefaceforthefirstvolumeofthenewseries“Compendium
of Plant Genomes”, a net search tells me that complete or nearly-complete
whole-genome sequencing of 45 crop plants, eight crop and model plants,
eight model plants, 15 crop progenitors and relatives, and three basal plants
areaccomplished,themajorityofwhichareinthepublicdomain.Thismeans
thatwenowadaysknowmanyofourmodelandcropplantschemically,i.e.,
directly,andwemaydepictthemandutilizethempreciselybetterthanever.
Genome sequencing has covered all groups of crop plants. Hence, infor-
mation on the precise depiction of plant genomes and the scope of their
utilization is growing rapidly every day. However, the information is scat-
tered in research articles and review papers in journals and dedicated web
pages of the consortia and databases. There is no compilation of plant gen-
omes and the opportunity of using the information in sequence-assisted
breeding or further genomic studies. This is the underlying rationale for
starting this book series, with each volume dedicated to a particular plant.
Plant genome science has emerged as an important subject in academia,
and the present compendium of plant genomes will be highly useful both to
students and teaching faculties. Most importantly, research scientists
involvedingenomicsresearchwillhaveaccesstosystematicdeliberationson
the plant genomes of their interest. Elucidation of plant genomes is not
onlyofinterestforthegeneticistsandbreeders,butalsoforpractitionersofan
array of plant science disciplines, such as taxonomy, evolution, cytology,
PrefacetotheSeries ix
physiology, pathology, entomology, nematology, crop production, bio-
chemistry, and obviously bioinformatics. It must be mentioned that infor-
mation regarding each plant genome is ever-growing. The contents of the
volumes of this compendium are therefore focusing on the basic aspects
of the genomes and their utility. They include information on the academic
and/oreconomicimportanceoftheplants,descriptionoftheirgenomesfrom
amoleculargeneticandcytogeneticpointofview,andthegenomicresources
developed. Detailed deliberations focus on the background history of the
national and international genome initiatives, public and private partners
involved,strategiesandgenomicresourcesandtoolsutilized,enumerationon
thesequencesandtheirassembly,repetitivesequences,geneannotation,and
genome duplication. In addition, synteny with other sequences, comparison
of gene families, and, most importantly, potential of the genome sequence
informationforgenepoolcharacterizationthroughgenotypingbysequencing
(GBS) and genetic improvement of crop plants have been described. As
expected, there is a lot of variation of these topics in the volumes based on
the information available on the crop, model, or reference plants.
Imustconfessthatastheserieseditorithasbeenadauntingtaskformeto
work on such a huge and broad knowledge base that spans so many diverse
plant species. However, pioneering scientists with life-time experience and
expertise on the particular crops did excellent jobs editing the respective
volumes.Imyselfhavebeenasmallscienceworkeronplantgenomessince
the mid-1980s and that provided me the opportunity to personally know
several stalwarts of plant genomics from all over the globe. Most, if not all,
of the volume editors are my longtime friends and colleagues. It has been
highly comfortable and enriching for me to work with them on this book
series.Tobehonest,whileworkingonthisseriesIhavebeenandwillremain
a student first, a science worker second, and a series editor last. And I must
express my gratitude to the volume editors and the chapter authors for pro-
viding me the opportunity to work with them on this compendium.
Ialsowishtomentionhere mythanks andgratitude totheSpringerstaff,
Dr. Christina Eckey and Dr. Jutta Lindenborn in particular, for all their
constant and cordial support right from the inception of the idea.
I always had to set aside additional hours to edit books besides my pro-
fessional and personal commitments—hours I could and should have given
to my wife, Phullara, and our kids, Sourav, and Devleena. I must mention
that they not only allowed me the freedom to take away those hours from
them but also offered their support in the editing job itself. I am really not
sure whether my dedication of this compendium to them will suffice to do
justice to their sacrifices for the interest of science and the science
community.
Kalyani, India Chittaranjan Kole
Preface to the Volume
Jatropha, Jatropha curcas L., a drought-tolerant shrub species of the
Euphorbiaceae family, has recently attracted people’s attention as a
promising biofuel crop. Seeds of jatropha contain non-edible oil that is
suitable to produce biodiesel or jet fuel. It is expected to contribute to
reductionofCO emissionbysubstitutingforfossil fuel,withoutcompeting
2
with the food crops. However, because it has been mainly used as a hedge
plantformanyyears,itsbreedinghistoryasacommercialbiofuelcropisnot
long enough. More extensive studies andbreedingeffortswouldberequired
formoreprofitablecommercialproduction.Genomesequenceinformationis
an important basis for further genetic studies and breeding. Jatropha is a
diploid species, and its estimated genome size is 416 Mb in n = 11 chro-
mosomes. Its first draft genome sequence was published in 2011, and since
then, more than 300 Mb of the jatropha genome sequence has been deter-
mined. Genomic and genetic studies, such as researches on QTL, tran-
scriptional factors, flowering genes, and DNA markers have made progress.
On the other hand, metabolomic and physiological studies have also been
done,whichareessentialtoimprovequalityandquantityoftheoil,andalso
to reduce or utilize toxic substances of seeds. To improve agronomic traits,
methodstogenerategeneticallymodifiedjatrophahavebeenestablished,and
useful transgenic jatropha plants have been developed based on the genetic
andphysiologicalstudies.Becausejatrophaisacommercialcrop,translation
ofthescientificachievements tothepracticaluse isimportant.Latest results
ofbreedingandstudiesonpracticalcultivationwouldbeindispensableforit.
The origin of jatropha was deciphered to be Mesoamerica, and only limited
genotypes in the Mesoamerican population have been brought to other
continents. Tracing dispersal routes of jatropha in the cultural aspect would
provideusefulinformationofthegeneticresourcesforbreeding.Thisvolume
includesachievementsinthesestudiesandprovidesanoverviewtoimprove
our understanding of jatropha from genomic, metabolomic, genetic, and
practical points of view. I thank all the authors for their excellent contribu-
tions to this volume and hope that all the chapters will help researchers and
breeders to study and improve this promising biofuel plant.
Suita, Japan Suguru Tsuchimoto
xi
